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- PDB-8ph0: Crystal structure of the metallo-beta-lactamase VIM1 with 3637 -

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Basic information

Entry
Database: PDB / ID: 8ph0
TitleCrystal structure of the metallo-beta-lactamase VIM1 with 3637
ComponentsBeta-lactamase VIM-1
KeywordsANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate
Function / homology: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / : / Beta-lactamase VIM-1
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsCalvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust099141/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the metallo-beta-lactamase VIM1 with 3637
Authors: Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J.
History
DepositionJun 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase VIM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6574
Polymers28,0511
Non-polymers6053
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-79 kcal/mol
Surface area9540 Å2
Unit cell
Length a, b, c (Å)39.460, 68.020, 40.290
Angle α, β, γ (deg.)90.000, 93.450, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase VIM-1 / Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta- ...Class B carbapenemase VIM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase VIM-1 / Metallobeta-lactamase / Subclass B1 metallo-beta-lactamase VIM-1 / VIM-1 / VIM-1 metallo-beta-lactamase / VIM-1 protein


Mass: 28051.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245 / Production host: Escherichia coli (E. coli) / Strain (production host): Q9XAY4 / References: UniProt: Q9XAY4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-YVO / 7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(2-oxidanylidene-1,3-dihydroindol-5-yl)-1~{H}-indole-2-carboxylic acid


Mass: 474.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2M ammonium phosphate 0.1M TrisHCl, pH 8.5 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.81532 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81532 Å / Relative weight: 1
ReflectionResolution: 1.36→39.39 Å / Num. obs: 45530 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 14.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 1.36→1.4 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3347 / CC1/2: 0.808 / R split: 0.745 / Rpim(I) all: 0.295 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→34.62 Å / SU ML: 0.1284 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.6121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1762 2184 4.8 %
Rwork0.1437 43318 -
obs0.1454 45502 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 1.36→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 37 315 2083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772058
X-RAY DIFFRACTIONf_angle_d1.10172854
X-RAY DIFFRACTIONf_chiral_restr0.0829316
X-RAY DIFFRACTIONf_plane_restr0.0111388
X-RAY DIFFRACTIONf_dihedral_angle_d8.3884319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.27041490.19412704X-RAY DIFFRACTION99.96
1.39-1.420.17891430.16922656X-RAY DIFFRACTION99.96
1.42-1.460.22831270.15772723X-RAY DIFFRACTION99.96
1.46-1.50.2029860.15992737X-RAY DIFFRACTION100
1.5-1.540.22621170.13652742X-RAY DIFFRACTION99.93
1.54-1.590.18251540.13342681X-RAY DIFFRACTION100
1.59-1.650.16991420.13162722X-RAY DIFFRACTION100
1.65-1.710.17541160.12642728X-RAY DIFFRACTION100
1.71-1.790.17461430.12132687X-RAY DIFFRACTION99.93
1.79-1.890.14761520.12052696X-RAY DIFFRACTION99.96
1.89-20.15151070.13812693X-RAY DIFFRACTION98.52
2-2.160.15951340.1252704X-RAY DIFFRACTION100
2.16-2.380.18211340.14012684X-RAY DIFFRACTION98.39
2.38-2.720.19491490.13772713X-RAY DIFFRACTION99.86
2.72-3.430.181470.14972723X-RAY DIFFRACTION100
3.43-34.620.16731840.15912725X-RAY DIFFRACTION99.9

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